It is known that N-methyl-D-aspartate (NMDA) receptor is essential for early brain development. NMDA receptor blockade during neonatal period causes various abnormal behaviors in later life. In the developing brain, NR2A- and NR2B-containing NMDA receptors show different expression patterns. However, the functions of these NMDA receptors in brain development are unknown. Therefore, we investigated the effects of pharmacological inactivation of NR2A- and/or NR2B-containing NMDA receptors on various behaviors in adulthood. We postnatally treated rats with an NR2A-preferring (PEAQX), an NR2B-selective (ifenprodil), or a nonselective NMDA receptor blocker (MK-801). Interestingly, neonatal treatment with PEAQX or MK-801 caused significant decrease in spontaneous alternation in the Y-maze test. In addition, PEAQX or MK-801 treatment increased startle response to acoustic stimuli. Neonatal PEAQX treatment also induced hypersensitivity to locomotor-stimulating effect of MK-801. On the other hand, neonatal ifenprodil treatment did not cause these behavioral alterations. Furthermore, PEAQX-treated but not ifenprodil-treated rats exhibited deformity of the hippocampal CA1 area, while neonatal NMDA receptor blockade did not alter the cell density in the hippocampus. In conclusion, our results suggest that the NR2A-containing NMDA receptor plays important roles in early brain development in rats, and hypofunction of this subunit during developmental period induces schizophrenia-related behaviors in adulthood.